scholarly journals Bottom-up and top-down control of dispersal across major organismal groups: a coordinated distributed experiment

2017 ◽  
Author(s):  
Emanuel A. Fronhofer ◽  
Delphine Legrand ◽  
Florian Altermatt ◽  
Armelle Ansart ◽  
Simon Blanchet ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Local Population ◽  
Space Use ◽  
Life History Trait ◽  
Population Fluctuations ◽  
Top Down ◽  
Bottom Up ◽  
Ecological Forecasting ◽  
Cascading Effects ◽  
Wide Range

AbstractOrganisms rarely experience a homogeneous environment. Rather, ecological and evolutionary dynamics unfold in spatially structured and fragmented landscapes, with dispersal as the central process linking these dynamics across spatial scales. Because dispersal is a multi-causal and highly plastic life-history trait, finding general drivers that are of importance across species is challenging but highly relevant for ecological forecasting.We here tested whether two fundamental ecological forces and main determinants of local population dynamics, top-down and bottom-up control, generally explain dispersal in spatially structured communities. In a coordinated distributed experiment spanning a wide range of actively dispersing organisms, from protozoa to vertebrates, we show that bottom-up control, that is resource limitation, consistently increased dispersal. While top-down control, that is predation risk, was an equally important dispersal driver as bottom-up control, its effect depended on prey and predator space use and whether dispersal occurred on land, in water or in the air: species that routinely use more space than their predators showed increased dispersal in response to predation, specifically in aquatic environments. After establishing these general causes of dispersal, we used a metacommunity model to show that bottom-up and top-down control of dispersal has important consequences for local population fluctuations as well as cascading effects on regional metacommunity dynamics. Context-dependent dispersal reduced local population fluctuations and desynchronized dynamics between communities, two effects that increase population and community stability.Our study provides unprecedented insights into the generality of the positive resource dependency of dispersal as well as a robust experimental test of current theory predicting that predator-induced dispersal is modulated by prey and predator space use. Our experimental and theoretical work highlights the critical importance of the multi-causal nature of dispersal as well as its cascading effects on regional community dynamics, which are specifically relevant to ecological forecasting.

scholarly journals Adaptive genetic variation mediates bottom-up and top-down control in an aquatic ecosystem

2015 ◽  
Vol 282 (1812) ◽  
pp. 20151234 ◽  
Author(s):  
Seth M. Rudman ◽  
Mariano A. Rodriguez-Cabal ◽  
Adrian Stier ◽  
Takuya Sato ◽  
Julian Heavyside ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Intraspecific Variation ◽  
Phenotypic Variation ◽  
Evolutionary Dynamics ◽  
Trophic Levels ◽  
Community Genetics ◽  
Top Down ◽  
Black Cottonwood ◽  
Bottom Up

Research in eco-evolutionary dynamics and community genetics has demonstrated that variation within a species can have strong impacts on associated communities and ecosystem processes. Yet, these studies have centred around individual focal species and at single trophic levels, ignoring the role of phenotypic variation in multiple taxa within an ecosystem. Given the ubiquitous nature of local adaptation, and thus intraspecific variation, we sought to understand how combinations of intraspecific variation in multiple species within an ecosystem impacts its ecology. Using two species that co-occur and demonstrate adaptation to their natal environments, black cottonwood ( Populus trichocarpa ) and three-spined stickleback ( Gasterosteus aculeatus ), we investigated the effects of intraspecific phenotypic variation on both top-down and bottom-up forces using a large-scale aquatic mesocosm experiment. Black cottonwood genotypes exhibit genetic variation in their productivity and consequently their leaf litter subsidies to the aquatic system, which mediates the strength of top-down effects from stickleback on prey abundances. Abundances of four common invertebrate prey species and available phosphorous, the most critically limiting nutrient in freshwater systems, are dictated by the interaction between genetic variation in cottonwood productivity and stickleback morphology. These interactive effects fit with ecological theory on the relationship between productivity and top-down control and are comparable in strength to the effects of predator addition. Our results illustrate that intraspecific variation, which can evolve rapidly, is an under-appreciated driver of community structure and ecosystem function, demonstrating that a multi-trophic perspective is essential to understanding the role of evolution in structuring ecological patterns.

scholarly journals Community venomics reveals intra-species variations in venom composition of a local population of Vipera kaznakovi in Northeastern Turkey

2018 ◽  
Author(s):  
Daniel Petras ◽  
Benjamin-Florian Hempel ◽  
Bayram Göçmen ◽  
Mert Karis ◽  
Gareth Whiteley ◽  
...  
Keyword(s):  
Snake Venom ◽  
Local Population ◽  
Venom Gland ◽  
Intact Protein ◽  
List Type ◽  
Snake Venoms ◽  
Top Down ◽  
Bottom Up ◽  
Venom Composition ◽  
Snake Bites

AbstractWe report on the variable venom composition of a population of the Caucasus viper (Vipera kaznakovi) in Northeastern Turkey. We applied a combination of venom gland transcriptomics, as well as de-complexing bottom-up and top-down venomics, enabling the comparison of the venom proteomes from multiple individuals. In total, we identified peptides and proteins from 15 toxin families, including snake venom metalloproteinases (svMP; 37.8%), phospholipases A2 (PLA2; 19.0%), snake venom serine proteinases (svSP; 11.5%), C-type lectins (CTL; 6.9%) and cysteine-rich secretory proteins (CRISP; 5.0%), in addition to several low abundant toxin families. Furthermore, we identified intra-species variations of the V. kaznakovi venom composition, and find these were mainly driven by the age of the animals, with lower svSP abundance in juveniles. On a proteoform level, several small molecular weight toxins between 5 and 8 kDa in size, as well as PLA2s, drove the difference between juvenile and adult individuals. This study provides first insights into venom variability of V. kaznakovi and highlights the utility of intact mass profiling for a fast and detailed comparison of snake venoms of individuals from a community.Biological SignificancePopulation level and ontogenetic venom variation (e.g. diet, habitat, sex or age) can cause a loss of antivenom efficacy against snake bites from wide ranging snake populations. The state of the art for the analysis of snake venoms are de-complexing bottom-up proteomics approaches. While useful, these have the significant drawback of being time-consuming and following costly protocols, and consequently are often applied to pooled venom samples. To overcome these shortcomings and to enable rapid and detailed profiling of large numbers of individual venom samples, we integrated an intact protein analysis workflow into a transcriptomics-guided bottom-up approach. The application of this workflow to snake individuals of a local population of V. kaznakovi revealed intra-species variations in venom composition, which are primarily explained by the age of the animals, and highlighted svSP abundance to be one of the molecular drivers for the compositional differences.HighlightsFirst community venomic analysis of a local population of the Caucasian viper (Vipera kaznakovi).The venom gland transcriptome of V. kaznakovi identified 46 toxin genes relating to 15 venom toxin families.Bottom-up venomics revealed the identification of 25 proteins covering 7 toxin families mainly dominated by snake venom metalloproteinases (svMP).Community venomics by top-down mass profiling revealed ontogenetic shifts between juvenile and adult snakes.

Special Issue on Texturing Processes and Attainable Functionalities

2016 ◽  
Vol 10 (1) ◽  
pp. 3-3
Author(s):  
Nobuyuki Moronuki
Keyword(s):  
Self Assembly ◽  
Special Issue ◽  
Top Down ◽  
Bottom Up ◽  
Energy Beam ◽  
Surface Functionality ◽  
Material Deposition ◽  
Wide Range ◽  
Lotus Leaves ◽  
Optical Applications

Regular micro/nanostructures or textures provide such functions as optical or friction properties, but neither texture design nor the texturing process has been well developed. Functional texture is often inspired by natural designs, with the microstructure on the surface of lotus leaves or the nanostructure on the bottoms of geckos’ feet often cited as examples. “Biomimetic” has become a keyword in state-of-the-art technologies. Processes are also important because functional textures require a wide range of structural dimensions, from nanometers to micrometers. Top-down processes such as cutting or energy beam processing are often used and are based on the copying principle. Bottom-up processes include the self-assembly of particles and the anodic oxidation of aluminum. As the principle behind bottom-up processes is completely different from that behind top-down processes, special attention is warranted. Furthermore, material deposition can effect drastic changes in surface functionality. This special issue features nine papers, including eight studies and one review paper, classified into the following topics: - Biomimetic design of functions - Top-down or cutting texturing processes - Bottom-up or self-organization texturing processes - Measurement system for textures - Optical applications - Optical applications - Adhesive applications - Biomedical applications These papers present the latest advances in texturing processes, functional design, and realization or demonstration. Learning more about these advances will enable readers toshare their knowledge and experience in technologies, development, and potential texturing applications. In closing, I would like to express my sincere gratitude to the authors and reviewers for their interesting and enlightening contributions to this special issue.

Cascading effects of larval Crucian carp introduction on phytoplankton and microbial communities in a paddy field: top-down and bottom-up controls

2011 ◽  
Vol 26 (3) ◽  
pp. 615-626 ◽  
Author(s):  
Yoko Nishimura ◽  
Taisuke Ohtsuka ◽  
Kohei Yoshiyama ◽  
Daisuke Nakai ◽  
Fujiyoshi Shibahara ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Paddy Field ◽  
Crucian Carp ◽  
Top Down ◽  
Bottom Up ◽  
Cascading Effects

scholarly journals Interaction between top-down and bottom-up control in marine food webs

2017 ◽  
Vol 114 (8) ◽  
pp. 1952-1957 ◽  
Author(s):  
Christopher Philip Lynam ◽  
Marcos Llope ◽  
Christian Möllmann ◽  
Pierre Helaouët ◽  
Georgia Anne Bayliss-Brown ◽  
...  
Keyword(s):  
Food Webs ◽  
North Sea ◽  
Time Series Data ◽  
Trophic Levels ◽  
Series Data ◽  
Resource Exploitation ◽  
Top Down ◽  
Bottom Up ◽  
Cascading Effects ◽  
Complex Patterns

Climate change and resource exploitation have been shown to modify the importance of bottom-up and top-down forces in ecosystems. However, the resulting pattern of trophic control in complex food webs is an emergent property of the system and thus unintuitive. We develop a statistical nondeterministic model, capable of modeling complex patterns of trophic control for the heavily impacted North Sea ecosystem. The model is driven solely by fishing mortality and climatic variables and based on time-series data covering >40 y for six plankton and eight fish groups along with one bird group (>20 y). Simulations show the outstanding importance of top-down exploitation pressure for the dynamics of fish populations. Whereas fishing effects on predators indirectly altered plankton abundance, bottom-up climatic processes dominate plankton dynamics. Importantly, we show planktivorous fish to have a central role in the North Sea food web initiating complex cascading effects across and between trophic levels. Our linked model integrates bottom-up and top-down effects and is able to simulate complex long-term changes in ecosystem components under a combination of stressor scenarios. Our results suggest that in marine ecosystems, pathways for bottom-up and top-down forces are not necessarily mutually exclusive and together can lead to the emergence of complex patterns of control.

scholarly journals Top-Down and Bottom-Up Proteomics Methods to Study RNA Virus Biology

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 668
Author(s):  
Yogy Simanjuntak ◽  
Kira Schamoni-Kast ◽  
Alice Grün ◽  
Charlotte Uetrecht ◽  
Pietro Scaturro
Keyword(s):  
Mass Spectrometry ◽  
Protein Complexes ◽  
Rna Virus ◽  
Screening Methods ◽  
Structural Level ◽  
Top Down ◽  
Bottom Up ◽  
Wide Range ◽  
Antiviral Targets ◽  
Virus Biology

RNA viruses cause a wide range of human diseases that are associated with high mortality and morbidity. In the past decades, the rise of genetic-based screening methods and high-throughput sequencing approaches allowed the uncovering of unique and elusive aspects of RNA virus replication and pathogenesis at an unprecedented scale. However, viruses often hijack critical host functions or trigger pathological dysfunctions, perturbing cellular proteostasis, macromolecular complex organization or stoichiometry, and post-translational modifications. Such effects require the monitoring of proteins and proteoforms both on a global scale and at the structural level. Mass spectrometry (MS) has recently emerged as an important component of the RNA virus biology toolbox, with its potential to shed light on critical aspects of virus–host perturbations and streamline the identification of antiviral targets. Moreover, multiple novel MS tools are available to study the structure of large protein complexes, providing detailed information on the exact stoichiometry of cellular and viral protein complexes and critical mechanistic insights into their functions. Here, we review top-down and bottom-up mass spectrometry-based approaches in RNA virus biology with a special focus on the most recent developments in characterizing host responses, and their translational implications to identify novel tractable antiviral targets.

scholarly journals Toward a trophic theory of species diversity

2015 ◽  
Vol 112 (37) ◽  
pp. 11415-11422 ◽  
Author(s):  
John W. Terborgh
Keyword(s):  
Species Diversity ◽  
Rocky Intertidal ◽  
Alternative States ◽  
Top Down ◽  
Bottom Up ◽  
Top Predators ◽  
Resource Limited ◽  
Wide Range ◽  
Keystone Predation ◽  
Order Of Magnitude

Efforts to understand the ecological regulation of species diversity via bottom-up approaches have failed to yield a consensus theory. Theories based on the alternative of top-down regulation have fared better. Paine’s discovery of keystone predation demonstrated that the regulation of diversity via top-down forcing could be simple, strong, and direct, yet ecologists have persistently failed to perceive generality in Paine’s result. Removing top predators destabilizes many systems and drives transitions to radically distinct alternative states. These transitions typically involve community reorganization and loss of diversity, implying that top-down forcing is crucial to diversity maintenance. Contrary to the expectations of bottom-up theories, many terrestrial herbivores and mesopredators are capable of sustained order-of-magnitude population increases following release from predation, negating the assumption that populations of primary consumers are resource limited and at or near carrying capacity. Predationsensu lato(to include Janzen–Connell mortality agents) has been shown to promote diversity in a wide range of ecosystems, including rocky intertidal shelves, coral reefs, the nearshore ocean, streams, lakes, temperate and tropical forests, and arctic tundra. The compelling variety of these ecosystems suggests that top-down forcing plays a universal role in regulating diversity. This conclusion is further supported by studies showing that the reduction or absence of predation leads to diversity loss and, in the more dramatic cases, to catastrophic regime change. Here, I expand on the thesis that diversity is maintained by the interaction between predation and competition, such that strong top-down forcing reduces competition, allowing coexistence.

scholarly journals Facilitating a research culture in an academic library: top down and bottom up approaches

2016 ◽  
Vol 117 (1/2) ◽  
pp. 105-127 ◽  
Author(s):  
Miggie Pickton
Keyword(s):  
Academic Library ◽  
Professional Community ◽  
Practitioner Research ◽  
Research Culture ◽  
Top Down ◽  
Research Activity ◽  
Bottom Up ◽  
Content Type ◽  
Wide Range ◽  
The University

Purpose – The purpose of this paper is to consider why and how a research culture might be established in an academic library and to describe and evaluate efforts to achieve this at the University of Northampton. Design/methodology/approach – Contextualised within current literature on this topic, the paper examines the top-down and bottom-up approaches taken to facilitate practitioner research in one academic library. Findings – The approaches taken have led to a significant increase in practitioner research activity from library staff, resulting in a variety of enhancements to library services; a number of innovative practices being shared with the professional community through conference presentations and publications; and consequent rise in profile and reputation for individuals, the department and the university. Practical implications – The paper offers a wide range of ideas and practical suggestions for encouraging and facilitating practitioner research in an academic library. These include incorporating research activity into job descriptions and annual performance reviews; facilitating peer support for research; and providing competitive research awards, research training opportunities and funding for staff presenting at external events. Many of these require relatively little resource, yet offer significant benefit to those involved. Originality/value – It is rare, and maybe unique in the UK, for an academic library to attempt to instil a research culture throughout its staff and to provide ongoing resources, activities and practical support for this. The many positive outcomes from this work demonstrate its success and value. The experiences described in this paper are transferable to other academic and research libraries and, if replicated, have the potential to increase librarians’ engagement in research activity, promote research-informed practice and stimulate interest in library and information research across the sector.

scholarly journals Synthesis of graphene: Potential carbon precursors and approaches

2020 ◽  
Vol 9 (1) ◽  
pp. 1284-1314
Author(s):  
Yuxin Yan ◽  
Fathima Zahra Nashath ◽  
Sharon Chen ◽  
Sivakumar Manickam ◽  
Siew Shee Lim ◽  
...  
Keyword(s):  
Large Scale ◽  
Synthesis Method ◽  
Chemical Vapour ◽  
Synthesis Methods ◽  
Top Down ◽  
Bottom Up ◽  
Graphene Synthesis ◽  
Common Precursor ◽  
Wide Range ◽  
Fit For Purpose

Abstract Graphene is an advanced carbon functional material with inherent unique properties that make it suitable for a wide range of applications. It can be synthesized through either the top–down approach involving delamination of graphitic materials or the bottom–up approach involving graphene assembly from smaller building units. Common top–down approaches are exfoliation and reduction while bottom–up approaches include chemical vapour deposition, epitaxial growth, and pyrolysis. A range of materials have been successfully used as precursors in various synthesis methods to derive graphene. This review analyses and discusses the suitability of conventional, plant- and animal-derived, chemical, and fossil precursors for graphene synthesis. Together with its associated technical feasibility and economic and environmental impacts, the quality of resultant graphene is critically assessed and discussed. After evaluating the parameters mentioned above, the most appropriate synthesis method for each precursor is identified. While graphite is currently the most common precursor for graphene synthesis, several other precursors have the potential to synthesize graphene of comparable, if not better, quality and yield. Thus, this review provides an overview and insights into identifying the potential of various carbon precursors for large-scale and commercial production of fit-for-purpose graphene for specific applications.

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